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Saturday, February 18, 2012

I was using Windows 7. I had a hard drive containing multiple partitions. I was in the habit of booting with an Ubuntu Live CD, now and then, to get a GParted view of the drive's condition. GParted would quickly show me problems with partitions, in a way that seemed superior to what I could get in Windows.

(I was new to Ubuntu 11.10. Unlike earlier versions, there was no longer an option to start GParted via an easy menu pick, which as I recalled was System > Information > Gparted. I found it in 11.10 by mousing to the top left button (tooltip: "Dash Home") and doing a search for GParted. Once I did that, the Live CD temporarily added it to the toolbar stretching down the left side of the screen.)

This time, GParted gave me the surprising information that the entire drive (which I had just been using, minutes earlier) was unallocated; and when I took a closer look via the right-click Information option, GParted said, "Can't have overlapping partitions." This post discusses this situation. (The processes described here unfolded over a period of some days, so there may be some discontinuities in the account, but I think the basic picture comes through.)

I began with a broad search and then a narrower one. These included repeated suggestions that I go into Terminal (available via search, and also down toward the bottom of the left-side button bar, as above) and type "sudo fdisk -lu." (That's a -LU, not -1U.) I had a couple of drives, and thus had to enlarge the Terminal window (or scroll back up) to see what it was saying about /dev/sda, which was the drive GParted had considered problematic. As I looked down the list of what fdisk was telling me about partitions, I couldn't figure out what GParted was complaining about. What I expected to see was something like this:

Device Start End
/dev/sda1 63 5000000
/dev/sda2 4999999 8000000

In that example, sda2 would start before sda1 ended. But I didn't see anything like that. The numbers in my list made sense. I also didn't have an error message in my list, like that shown by one user: "Partition 1 does not end on cylinder boundary." A later post in that thread suggested typing this in Terminal:

sudo parted /dev/sda unit s print

That just gave me the same "Error: Can't have overlapping partitions" message. This was to be expected: GParted was a front end to parted. This was just two ways of getting the same report from the same program.

The problem identified in another thread was in the total disk size reported by fdisk. The top part of the fdisk output said there was a total of 312581808 sectors in /dev/sda, but the list of individual partitions said that the extended partition (and a logical partition within it) ended at 312590879. The latter was a bigger number than the former. That is, the partitions were supposedly continuing on past the end of the drive. There was also a discrepancy between an early line in the fdisk output, which said that sector size was 512 bytes, and a later line, which said that sector size was 2048 bytes. The advice given in that thread was to use fdisk to delete and recreate the partitions with the correct size. I would have been inclined to use GParted for that, as it seemed easier, but on reflection I realized that I had probably used GParted to create these partitions in the first place. But I guess I could have used GParted and then tested it with fdisk again.

But anyway, I didn't have those problems. The numbers in my fdisk output made sense. So far, no answer. I drifted through another thread that pointed me toward TestDisk. Typing "TestDisk" in Terminal told me that I would have to install the "universe" repository of program downloads in order to install TestDisk. This might not have been a problem with an installed copy of Ubuntu but I wasn't sure how to do that with a live CD in Ubuntu 11.10. It appeared that I might have to remaster my Live CD to include the universe repository. That seemed to be getting pretty far away from the original mission.

It occurred to me that I ought to be able to get similar output from a Windows program -- to see a list of partitions and sectors like that which I could see in fdisk in Ubuntu. This would not be CHKDSK, which would check the file structure within a partition. At the moment, I wasn't sure what program I would use for that purpose.

Before I could pursue that thought, I looked again at the fdisk output. Now I saw something I hadn't noticed before. My last partition did not go beyond the end of the drive. But it did go beyond the end of the extended partition. In other words, I was supposed to have this arrangement: Primary Partition 1, Primary Partition 2 (optional), Primary Partition 3 (optional), and then either Primary Partition 4 or Extended Partition; and the Extended Partition was supposed to contain any additional (logical) partitions -- up to the end of the drive, usually. Mine didn't do that. The relevant lines from fdisk -lu looked like this:

Device Start End
/dev/sda3 7000000 9000000
/dev/sda8 8000000 9500000

In the System column provided by fdisk (not shown here because of insufficient line space), sda3 was the extended partition. In other words, these numbers were saying that dev8 was starting inside the extended partition, as it should; but it was ending after the extended partition, and that was improper. It wasn't a question of GParted not being reliable, as I had begun to fear. GParted appeared to be identifying a legitimate issue. But GParted wasn't going to help me fix it: as noted above, it was showing the whole drive as being unallocated, which was incorrect, and the only option it was offering me was to create a new partition in that big unallocated space -- that is, wipe out all my data and partitions on that drive.

I was thinking that I should double-check GParted using a Windows tool, and that anyway it would be nice to have a Windows-type alternative to this Ubuntu tool. I assumed Microsoft itself would not be inclined to give me something useful for this purpose. The last partition was a Linux partition, not a Windows partition -- using ext3 format, I believed, not NTFS -- and Microsoft was not known for doing much that would be helpful in the Linux world.

It seemed that I would have to use fdisk, from the Ubuntu CD. I wasn't entirely sure how to proceed. Fdisk was giving information in terms of "blocks," but when I typed "fdisk" by itself at the command prompt, it gave me options in terms of cylinders, heads, or sectors per track, but not blocks.

Then again, as I thought about it, I realized that I actually could go into Windows > diskmgmt.msc and delete that ending Linux partition. Disk Management did display it. It surprised me that, if I wanted to use a GUI tool rather than a command-line option like fdisk, the tools offered in the Windows operating system would be more helpful, in this case, than those offered by Ubuntu.

I had been able to see that ending partition in GParted previously. It had been marked in some way to indicate that it was problematic. Why had GParted ceased to display it that way? It occurred to me to boot up with an older Ubuntu CD -- version 10.04 rather than 11.10. I did that and went into System > Administration > GParted. But no, it was showing "unallocated" too. So something had changed. GParted was wrong, and I was definitely going to have to use another tool to fix the situation.

Before taking the plunge into fdisk, I decided to use this opportunity to play with one or two other partitioning utilities I had burned to CD. One was Minitool Partition Wizard. It got a glowing Editor's Review and four stars from 389 voters at CNET. Unfortunately, it produced "Boot failed: press a key to retry" when I tried to boot my machine with the CD I had burned. Oops. Same thing on retry. Well, evidently it was time to download a newer copy. They were up to version 7.0.

While that was downloading, it turned out that I had another copy of Minitool Partition Wizard CD, version 5.2. I tried that. It loaded OK, and it showed the partitions without a problem. It was also faster and easier to get to the information, using a dedicated partition CD, instead of having to load Ubuntu and find GParted.

So, OK, this was looking promising. In Partition Wizard, I selected the appropriate drive and clicked the "Show Disk Properties" option. It didn't report errors. I wasn't sure if it was even capable of reporting errors. It said that that last, troublesome partition was actually unallocated space. As I recalled, I had formatted that partition to be ext3, in case I wanted somewhere to install Ubuntu. Maybe the Linux partition had deteriorated somehow; maybe that's why it was now problematic.

I decided I could do without that Ubuntu partition. Since I knew there was nothing in it, I told Partition Wizard to extend the preceding partition to take over this allegedly unallocated space. But not all of it. I had become superstitious about running partitions right up to the ends of drives. Just for good luck, I made that unallocated space into an NTFS drive. Partition Wizard decided that the last 14MB of that space would have to remain unallocated. I clicked Apply. Then I deleted the partition I had just made and replaced it with a relatively small (3GB) ext3 partition (which would not show up in Windows, just in case "unallocated" was a potentially troublesome status at drive's end), putting the rest of the space into the preceding partition.

That last step didn't go swimmingly. Partition Wizard said that it had "Failed to execute the following command" with "Error Code 36': Minitool Partition Wizard detects that file system of the partition have errors. Please use 'Check File System' function to fix it first." Ah, so there was a tool of that sort lurking there somewhere in Partition Wizard. But where? Now I saw why it hadn't popped out at me earlier: it was in the Partition menu (and also the context menu), but it was greyed out. I couldn't very well check the file system with a greyed-out tool. It didn't seem willing to run on any partition or drive on that computer.

By this point, the download of Partition Wizard version 7 had completed on the working machine, so I installed it there and took a look at it. Apparently it would work, for at least some purposes, while Windows was running. I doubted it would help the troubled computer, since the partition that I was trying to resize contained my paging file. The Check File System option was not greyed out. But now it seemed that, if I wanted a bootable CD, I had downloaded the wrong thing. The Minitool page for the bootable CD didn't specify that the bootable CD ISO would give me the Check File System option, but I decided to give it a whirl. I downloaded that ISO and tried to burn it to a blank DVD. ImgBurn said, "Invalid or unsupported image file format! Reason: First image file part is less than 2048 bytes in size." So, OK, bad download. I re-downloaded the ISO and tried again. It was a slow download. This time, when I tried to boot the newly burned DVD, I got "Unknown keyword in configuration file:" followed by eight junk characters and then "Could not find kernel image: linux." I tried a cold boot but still got the same thing. This DVD was junk. I looked for other sites to download the ISO from, but they seemed to be the kinds of sites that would install malware.

I did want a bootable CD alternative to GParted, for situations like this. I looked into Parted Magic, but it didn't sound like it had the power of GParted. Their Live USB option had TestDisk, though, and would apparently only take about 45MB, so I thought it might be a good option to put on an old 256MB USB drive. I started up UNetbootin and pointed it toward Distribution > Parted Magic > Latest_Live. I had already plugged in my USB drive, so I chose that, and indicated that I wanted to reserve 50MB for files to be preserved across Ubuntu reboots. (I wasn't sure exactly what that was about, but it sounded good.) It started the process of downloading and installing whatever it needed, onto my USB drive. It said the download would be 175GB. Larger than expected. I decided to install from an ISO instead, so that I wouldn't have to re-download if the first try didn't succeed. So I downloaded the Parted Magic ISO and then went through the UNetbootin installation process that way.

While that was in play, I rebooted the troubled machine and went into Windows > Start > Run > diskmgmt.msc. As expected, Disk Management reported no drive problems. It showed all my partitions, including the smallish ending partition I had set aside for some possible future Ubuntu installation. I right-clicked on the partition adjacent to the ending partiiton, which Disk Management showed as "unallocated." There was an option to "Extend Volume." I went partway through that. It looked like Windows 7 was ready to fix the problem.

I installed Partition Wizard on the troubled machine. I wondered whether it would perform differently than the bootable CD version (above). It looked like it, too, was ready to go. Why was life so hard for had the CD? Another highly recommended alternative was Easeus Partition Master. I downloaded it from CNET (four stars, 943 voters) and installed it. Same thing there: the Windows installed version saw the partitions as expected, and seemed prepared to merge or resize as desired. But their "Bootable CD" option took me to a webpage that said the free version -- what I had just installed -- wouldn't include a bootable disk option.

By this point, the UNetbootin process was nearly done. But I decided to reboot with the Ubuntu 11.10 CD to test some other drives first. To my surprise, GParted was now showing everything as being OK on the previously troubled machine. Had we fixed something when I wasn't looking? And now I saw what the problem was -- why I'd gotten that funky fdisk output (above). The last partition on the disk, the one that I had set aside as unallocated, was not in the extended partition. It was a primary partition. Somehow, I had gotten myself into this arrangement: Primary Partition 1, Primary Partition 2, Extended Partition, and then Unallocated space outside of the extended partition.

Well, I didn't want that, especially not if it was going to confuse GParted or anyone else. It looked like I was going to have to wipe out the extended partition -- what's 900GB, between friends? -- and rebuild the thing, and have no excuse to test my cool new bootable USB version of Parted Magic (sniff!). Then it occurred to me to wonder what those Windows programs -- Disk Management and Easeus and Partition Wizard -- were planning to do with this situation. Were they somehow going to merge that last unallocated space into the extended partition, in some way that GParted wouldn't do?

Or, no, wait. I was trying to get GParted to merge the unallocated space directly into the last logical partition. That's not how these things are done. I needed to merge the unallocated space into the extended partition, and then shuffle that space on down the line, inside the extended partition, to whatever logical drive was most deserving. Is that what Windows Disk Management was planning to do?

I decided to find out, because if Windows could walk & chew partitions at the same time, I could meanwhile use the troubled machine to work on other things. Boot back into Win7; back into Disk Management; extend the volume. It took ... about seven seconds. Kind of ridiculous. I checked it with a GParted reboot. Now GParted was reporting a single partition filling the entire drive, plus a 1MB partition at the end.

Some days had passed since I had started the processes described in this post, and I wasn't entirely clear on exactly what I had done as I reviewed my notes (above). But I was sure I had set up an empty ending partition, in my superstition that having a little space at the end could sometimes prevent problems, and 1MB sounded like a possibility.

But in any case, the question had recurred: why was GParted not seeing the multiple partitions that I had just been working in, in Windows?

I decided to try out the bootable Parted Magic USB drive that UNetbootin had concocted for me. I made sure my BIOS was set to boot USB-ZIP first (instead of USB-FDD or USB-CDROM), and proceeded to boot that Parted Magic USB. Its boot menu gave me choices between the default, which would run from RAM, and a couple of bootup alternatives, in case my system had less than 312MB of RAM. It also gave me submenus for Extras, Failsafe, and RAID. The Extras menu contained options to load various hardware diagnostics (e.g., Hardware Detection Tool, Memtest86+) and boot managers (e.g., GRUB, GRUB2).

I loaded the default (which, as I soon discovered, would load automatically after 20 seconds if I didn't make a selection). This gave me an impressive desktop: Parted Magic was offering me at least 20 to 30 utilities (e.g., Disk Health, Monitor Settings, File Manager) plus Firefox. I was surprised they were able to squeeze so much onto one little USB drive. I tried out the Firefox: it worked. This definitely seemed like a tool worth having.

But then it seemed that maybe I had played with the Parted Magic boot menus too much. After a first or second reboot, the graphics became kind of buzzy (i.e., unexpected colored dots flashing in various colored spots, and along random horizontal and vertical lines) and off-centered (i.e., with a couple inches of black space on the left edge of the monitor) and began flashing on and off (i.e., intermittent black screen). I tried a cold boot (i.e., shut the machine down for at least 30 seconds before restarting, to clear memory). (Incidentally, the shutdown menu gave me the option of saving my current Parted Magic session. I guessed that this option was possible on a USB drive, which would have space to store such information, but might not have been available on a bootable Parted Magic CD.) But when I rebooted, I got two unexpected results: the USB drive did not boot -- instead, I went into Windows -- and now the buzzy and off-center graphics were affecting Windows too. Hmm ... probable hardware issue. I tried rebooting with an Ubuntu DVD, without the USB drive plugged in. But no, same thing there. It seemed to be getting worse: the black spells were longer. A monitor reset didn't help. I connected the monitor to a different computer. It worked OK there. I tried doing a longer cold shutdown -- several minutes -- and booting again, still without the USB drive plugged in. That worked. Now I got a normal Ubuntu screen. I tried booting the USB drive again. Now it worked. Without further ado, I went straight into its Partition Editor. But that turned out to be just GParted. It showed the same thing as GParted had shown when run from the Ubuntu Live CD. And I was getting the funky graphics again, and had to do another five-minute shutdown.

I had not yet succeeded in finding a bootable freeware CD or USB drive that would give me a believable impression of the partitions existing on that hard drive. I booted into Windows to take a look with the installed (as distinct from bootable) versions of Easeus and Minitool that I had installed there. I expected them to provide a realistic picture, even if all they did was to parrot what Windows was detecting (i.e., multiple NTFS partitions on that drive). But now, even after a 10-minute shutdown, the graphics were still buzzy, off-centered, and flashing (indeed, mostly) black.

What in the world had happened? I was tempted to try the bootable USB drive in another computer, to see whether it was the cause of this, but then I decided I really didn't want two messed-up computers. It did appear that the USB drive had caused it; there had never before been anything of this nature. The screen was totally black by now. I had to do a hard reset to see anything. I wasn't getting any distortion at the bootup phase. I tried loading the fail-safe defaults in the BIOS. I got an option to boot into Safe Mode, so I tried that. I was still getting some buzziness there. I tried Control Panel > Device Manager > Display Adapters > right-click on the adapter > Update Driver Software. It said my software was up to date. I tried right-click > Uninstall the display adapter (but not its driver software). A reboot into Normal Mode still showed some buzziness here and there (e.g., in a CMD window). I went back into Device Manager. Instead of Display Adapter, I had Other Devices > Video Controller (VGA Compatible). After five minutes or so, I saw a balloon tip telling me that the drivers specific to my video adapter (ATI Radeon HD 4250) had installed successfully, and now that device was visible as a Display Adapter in Device Manager. But apparently that took us back to the Dark Ages. After a reboot, the screen was black.

I rebooted into Safe Mode, hoping to do a System Restore. Funny thing: the login screen wasn't taking keyboard input. I couldn't enter my password. Even if I typed the password and hit Enter, the login screen did not change. I rebooted and tried the same thing in Normal Mode, though this time I was entering the password into a black screen. (I saw a flash of the login screen before it went black.) I got a Microsoft happy sound, which as I recalled indicated that I had succeeded in logging in. But the screen remained dark. Moving the mouse, hitting WinKey, etc. brought no joy. I could see the hard drive light burning away -- there was obviously a lot going on -- but I was blind to it all.

The monitor had VGA and DVI ports. It was connected via DVI. I thought I should try a VGA cable and see if that made a difference. This transition led to the culprit: loose DVI connector. No VGA necessary. Sorry for slandering the good name of the Parted Magic bootable USB drive. I mean, it still had GParted, and thus continued to be useless for present purposes in that regard. But at least it hadn't completely fubared my graphics circuits. At least not as far as I could tell.

Back in Windows Normal Mode, I started Easeus Partition Master 9.1 and MiniTool Partition Wizard Home Edition 7.1, both in their installed forms. Both saw the multiple partitions on that drive that GParted had been unable to see. Minitool listed them in alphabetical order by name; Easeus listed them in the preferred alphabetical order by drive letter. Easeus did, and MiniTool did not, show an 1.6MB unallocated partition at the end of that drive. Both appeared to be glorified and perhaps enhanced versions of Windows Disk Management. Both provided an indication as to whether a given partition was primary or extended.

On the drive in question (unlike another drive in that machine), both Easeus and MiniTool were listing the partitions as neither primary nor logical, but rather as "simple" partitions. I hadn't paid much attention to the difference until now. I didn't recall requesting any simple partitions; I had always just used primary and extended. I guessed that Windows Disk Management had converted the primary and extended partitions previously visible in GParted to simple partitions in that little seven-second operation where it "resolved" the previous situation. The general idea was that there were dynamic disks with simple partitions, and there were basic disks with primary and extended partitions, but the two did not mix: you could not have a dynamic disk with a primary or extended partition, or a basic disk with a simple partition.

It seemed that GParted was unable to work with simple partitions. Another way to say this was apparently that GParted would work only with basic (not dynamic) volumes, and the latter was what Disk Management had given me. I noticed that MiniTool did, but Easeus did not, provide a right-click option to resize a partition, also available in Windows Disk Management.

A search led to a MiniTool webpage that said MiniTool could convert a dynamic drive back to a basic drive without data loss. (Of course, one could always wipe and recreate partitions and then restore data from backup, assuming backup existed.) It looked like I would have to buy the pro version to get this capability. Another thread said that this wasn't possible without data loss via Acronis products, though one person did interject that a bit of expert-level hex editing could do it pretty easily. (I suspected that, if it were that easy, these programs would have been offering the capability, but maybe that was exactly what Minitool was doing.) The MiniTool webpage said that Partition Magic could do it. I had used PartitionMagic for years, almost always with good results, but thought it was defunct and incompatible with Windows 7. (Symantec had bought a good program and let it go to pot.) So I wasn't quite sure what that MiniTool page was trying to say.

I was out of time for researching this issue. My present impression was that I could (a) stay with the dynamic disk and use Windows Disk Management or the free MiniTool to resize or delete its simple partitions as needed; or (b) backup and wipe the drive, and then create a basic drive and fill it with primary and extended partitions, using virtually any of these tools, including GParted; or (c) buy the pro version of MiniTool and try converting the simple partition to primary without data loss; or (d) explore that expert editing approach to convert the partition manually.

My principal reason for wanting to be able to use GParted was to have a non-Windows perspective on what was happening on the drives. This was useful in two regards. First, until Windows converted the basic disk to a dynamic disk, I had been able to see partition information (with GParted and also with fdisk) and get insight into possible problems on my drive. Second, GParted gave me a very quick heads-up as to whether there were problems on a drive that would call for CHKDSK /R. Without GParted, I just ran CHKDSK /R on each partition. It was a very slow and inconvenient process, but I had the impression that it was better than just using the disk tools available within Windows drive properties. Its inconvenience tended to discourage doing it. Being able to book GParted (with or without Ubuntu) and take a quick look seemed to encourage more often disk checks. Typically, there would be no more than one partition needing this attention.

I decided that it would be easier to stay with the dynamic disk, at least for now, and that doing so would give me a chance to learn something about that kind of disk and its simple volumes. I just had to remember that this was why I was getting those weird results from GParted. There was also the possibility of an eventual update from GParted or some other tool to handle these volumes.

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Well, that experiment came to a swift conclusion. I discovered that Acronis True Image Home was not able to see the dynamic drive or any of its simple partitions. Acronis had worked well for me. I didn't want to look for a replacement for it and for any other programs that would require a basic rather than dynamic disk. I made sure my backup was current, and then repartitioned the dynamic drive using GParted. It seemed I should not have used Windows Disk Management to adjust partitions.

I proceeded to wipe the dynamic disk, using Windows Disk Management to delete most of the individual partitions and then rebooting with Parted Magic on the USB drive to delete the rest. I found that GParted on that USB tool was not able to create partitions on the drive. It was giving me errors. I rebooted with a Ubuntu 11.10 DVD and tried GParted there. It was able to create the partitions with no problems.

Wow Ray ... a fully-fledged novel in blog format! Must have been some day you were having!

I came to your post looking for a solution to overlapping partitions. I had used Acronis (like you say - a usually very good tool), but it has left some problems on my hard drive after having to re-install Windows and shrink the Linux partitions I had. It now credits me with having a million or so TB ... If only!

Interesting article. I think if you do a search for overlapping partitions, you will find GParted mentioned a lot, but not for the reason most would suspect. GParted actually causes these overlaps - it's an acknowledged bug!!! Or was we are told, it was supposed to be fixed around version 0.12. I still have a couple of machines running Ubuntu 10.04 and the 'current' GParted version in the repositories still has this bug - which they actually rate as 'Medium' - which is a disgrace considering both its seriousness and the ease at which it can be built from source. Tell that to someone who has had healthy partitions mangled by GParted - like I did! And have again believe it or not - hence my trawling for info now! And this even though I had built GParted 0.14-1 which is supposed to be trouble-free in this regard. But the very same thing happened again and right after I had resized & added a logical partition to an extended one - the GParted Achilles heel. Right now, I have sorted out the overlapping problem but am faced with something even more ominous - a 'extended partition busy, kernel unaware of changes made' error. After much searching and although its widely posted about, not one seems to have been able to sort this problem, a fix that doesn't involve deleting partitions at any rate - not an option for me and anyway, there's no knowledge to be gained going in that direction. There has been a lot of mention of big-name disc tools here. One of the best first-stops imo is the Hiren CD. My version 14.1 has version 5 of Minitools on it, as well as countless others. And frankly I'm rather unimpressed with most of them. Disc Genius looked rather good, reporting errors where others saw green grass, but its 'fixes' either left the computer unbootable or drives were no longer automatically mounted on reboot. It also reported my ext4 install as being ext3 which is pretty uninspiring, especially for a commercial product. Better than many/most other M$ tools who list linux partitions as unknown/unallocated I suppose. I'm surprised that Testdisk wasn't mentioned. This superb little utility is free, caters for practically all-OS's and the only application that I know of that will fix the overlapping partitions problem. No fancy GUI (terminal app) and it can be a little hairy going at the start, but it does a terrific job. It's also great for file-recovery. Finally, if you alter the partition table in any appreciable way, your system will not boot, even when everything is done correctly. With Linux, you will then have to reinstall grub via Chroot. Excuse the length of this post, but maybe someone will glean something from it.